RNA viruses can adapt to new environments by introducing mutations in their genomes, which have resulted in the recent expansion of some viruses. After 60 years of exclusive circulation in Asia and Africa, chikungunya virus (CHIKV) has recently rapidly spread in Europe and the Americas. The authors were interested in the evolution of CHIKV in different hosts and found that there are host-specific requirements of the CHIKV 3’UTR. In particular, they found that sequence repeats are conserved at the CHIKV 3’UTR but vary in copy number among viral lineages. These blocks of repeated sequences may increase RNA recombination through a copy-choice mechanism that acts together with viral selection, leading to the emergence of new viral variants. When the authors functionally analysed a panel of mutant viruses they found that there were opposite selection pressures in mosquito and mammalian cells that impose a fitness cost during transmission. This fitness cost is alleviated by this recombination guided by sequence repeats. During the host switch there were significant changes in the frequency of viral variants with different numbers of repeats. Therefore it appears that this RNA recombination accelerates CHIKV adaptability, allowing the virus to overcome genetic bottlenecks within the mosquito host.
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